Variant report

Variant	rs2304589
Chromosome Location	chr2:20101487-20101488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20100859-20102249	H1-neurons	neurons:	n/a	n/a
2	ELF1	chr2:20101335-20101839	K562	blood:	n/a	chr2:20101439-20101451
3	ZBTB33	chr2:20100950-20102238	HepG2	liver:	n/a	chr2:20101452-20101461 chr2:20101760-20101769
4	CTCF	chr2:20101422-20101562	Hela-S3	cervix:	n/a	chr2:20101426-20101435
5	TAF1	chr2:20101023-20102113	HepG2	liver:	n/a	n/a
6	ATF1	chr2:20101350-20102179	K562	blood:	n/a	n/a
7	PML	chr2:20100762-20102440	K562	blood:	n/a	n/a
8	TAF1	chr2:20101044-20102200	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr2:20100962-20101999	K562	blood:	n/a	chr2:20101080-20101089 chr2:20101865-20101872 chr2:20101081-20101088 chr2:20101080-20101092 chr2:20101081-20101088 chr2:20101081-20101088
10	CTCF	chr2:20101390-20101597	A549	lung:	n/a	chr2:20101426-20101435
11	POLR2A	chr2:20099750-20102696	K562	blood:	n/a	n/a
12	SIN3AK20	chr2:20100612-20102379	MCF-7	breast:	n/a	n/a
13	TCF7L2	chr2:20101230-20102040	Hela-S3	cervix:	n/a	n/a
14	HA-E2F1	chr2:20100884-20102205	MCF-7	breast:	n/a	chr2:20101080-20101089 chr2:20101865-20101872 chr2:20101081-20101088 chr2:20101080-20101092 chr2:20101081-20101088 chr2:20101081-20101088
15	POLR2A	chr2:20100820-20102117	GM10847	blood:	n/a	n/a
16	ZEB1	chr2:20101274-20102014	GM12878	blood:	n/a	n/a
17	KAT2A	chr2:20101394-20101977	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:20101230-20102193	HepG2	liver:	n/a	n/a
19	JUND	chr2:20101165-20102079	A549	lung:	n/a	n/a
20	CTCF	chr2:20101440-20101590	HAc	cerebellar:	n/a	n/a
21	BCLAF1	chr2:20100929-20102518	K562	blood:	n/a	chr2:20101437-20101450
22	REST	chr2:20101278-20101964	Hela-S3	cervix:	n/a	n/a
23	ZBTB33	chr2:20101143-20102073	GM12878	blood:	n/a	chr2:20101452-20101461 chr2:20101760-20101769
24	TBL1XR1	chr2:20101335-20102524	K562	blood:	n/a	n/a
25	ELF1	chr2:20101169-20102396	MCF-7	breast:	n/a	chr2:20101439-20101451
26	CEBPB	chr2:20101350-20102279	K562	blood:	n/a	n/a
27	NFIC	chr2:20101176-20102210	HepG2	liver:	n/a	n/a
28	PAX5	chr2:20101134-20101598	GM12892	blood:	n/a	chr2:20101377-20101387
29	FOSL2	chr2:20101064-20102382	A549	lung:	n/a	n/a
30	MAFK	chr2:20101282-20102029	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:20101116-20102142	SK-N-MC	brain:	n/a	n/a
32	NRF1	chr2:20101310-20101709	Hela-S3	cervix:	n/a	chr2:20101492-20101503
33	ELF1	chr2:20101275-20102228	HepG2	liver:	n/a	chr2:20101439-20101451
34	TEAD4	chr2:20101400-20102186	ECC-1	luminal epithelium:	n/a	chr2:20102116-20102125
35	ATF2	chr2:20101218-20102059	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAZ	chr2:20100989-20102091	Hela-S3	cervix:	n/a	n/a
37	REST	chr2:20101145-20102173	PFSK-1	brain:	n/a	n/a
38	TAF1	chr2:20101077-20102125	H1-neurons	neurons:	n/a	n/a
39	JUN	chr2:20101428-20102016	H1-hESC	embryonic stem cell:	n/a	n/a
40	ZBTB33	chr2:20101199-20102174	HepG2	liver:	n/a	chr2:20101452-20101461 chr2:20101760-20101769
41	POLR2A	chr2:20100927-20102350	ECC-1	luminal epithelium:	n/a	n/a
42	TEAD4	chr2:20100652-20102368	K562	blood:	n/a	chr2:20102116-20102125
43	TAF1	chr2:20101243-20102043	GM12892	blood:	n/a	n/a
44	FOXA2	chr2:20101262-20102034	HepG2	liver:	n/a	n/a
45	CREB1	chr2:20101232-20102192	H1-hESC	embryonic stem cell:	n/a	n/a
46	CREB1	chr2:20100814-20102634	K562	blood:	n/a	n/a
47	RELA	chr2:20099826-20102359	GM18505	blood:	n/a	n/a
48	POLR2A	chr2:20101008-20102537	GM12891	blood:	n/a	n/a
49	TAF1	chr2:20101127-20102206	K562	blood:	n/a	n/a
50	BRCA1	chr2:20101011-20102130	GM12878	blood:	n/a	chr2:20101760-20101769 chr2:20101452-20101461

No.	Distal block	Cell Line	Cell type
1	chr2:20101039..20101818-chr4:103790051..103790670,2	Hela-S3	cervix:
2	chr2:20101080..20101636-chr5:65439827..65440416,2	HCT-116	colon:
3	chr2:20099947..20101798-chr4:35496664..35498184,2	K562	blood:
4	chr2:20101248..20101831-chr20:2505073..2505680,2	Hela-S3	cervix:
5	chr2:20099437..20102980-chr2:20547960..20551663,4	K562	blood:
6	chr2:20100443..20102205-chr4:35495184..35498163,2	MCF-7	breast:
7	chr2:20099026..20101634-chr2:20189872..20192427,2	K562	blood:
8	chr2:20101258..20102240-chr5:16465669..16466217,3	Hela-S3	cervix:
9	chr2:20068233..20072834-chr2:20097586..20102817,5	K562	blood:
10	chr14:51410843..51411516-chr2:20101442..20102236,2	Hela-S3	cervix:
11	chr2:20101141..20101930-chr7:44529626..44530595,2	NB4	blood:
12	chr2:18740138..18743092-chr2:20100674..20102788,2	MCF-7	breast:
13	chr2:20100261..20103746-chr2:20249026..20255152,7	K562	blood:
14	chr2:20101237..20102018-chr3:159480945..159481897,2	Hela-S3	cervix:
15	chr1:28907796..28908626-chr2:20101327..20102014,2	Hela-S3	cervix:
16	chr2:20066730..20071387-chr2:20098933..20103374,5	MCF-7	breast:
17	chr15:71055917..71056560-chr2:20101389..20101997,2	Hela-S3	cervix:
18	chr1:144533619..144534549-chr2:20101329..20102307,3	Hela-S3	cervix:
19	chr11:71823521..71824098-chr2:20101368..20102233,2	Hela-S3	cervix:
20	chr2:20101059..20101595-chr2:44222918..44223626,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000271991	TF binding region
TTC32	TF binding region
ENSG00000015676	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000100504	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000153914	Chromatin interaction
ENSG00000228784	Chromatin interaction
ENSG00000137831	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000118965	Chromatin interaction
ENSG00000240857	Chromatin interaction
ENSG00000206665	Chromatin interaction
ENSG00000138095	Chromatin interaction
ENSG00000197989	Chromatin interaction
ENSG00000227210	Chromatin interaction
ENSG00000250588	Chromatin interaction
ENSG00000088876	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000223734	Chromatin interaction
ENSG00000173545	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10175236	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10175486	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10190645	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10203067	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10211513	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11096633	0.88[CEU][hapmap]
rs11887799	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12328613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467740	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12478941	0.94[CEU][hapmap]
rs12615824	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1462754	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16987206	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16987297	0.94[CEU][hapmap]
rs2278528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28742930	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3754907	0.87[CEU][hapmap]
rs3754908	0.87[CEU][hapmap]
rs3769763	0.83[CEU][hapmap]
rs58978345	0.84[AMR][1000 genomes]
rs6716854	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717139	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721754	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6757734	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
5	nsv522640	chr2:20098208-20109061	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2304589	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs2304589	TTC32	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20099000-20102600	Active TSS	GM12878-XiMat	blood
2	chr2:20099000-20103000	Active TSS	K562	blood
3	chr2:20099800-20102000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:20099800-20102400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:20099800-20102600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:20099800-20102600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:20099800-20102600	Active TSS	Aorta	Aorta
8	chr2:20099800-20102800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:20099800-20103200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:20100000-20102200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:20100000-20102200	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr2:20100000-20102400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:20100000-20102400	Active TSS	Ovary	ovary
14	chr2:20100000-20102400	Active TSS	A549	lung
15	chr2:20100000-20102600	Active TSS	Thymus	Thymus
16	chr2:20100000-20102600	Active TSS	NHDF-Ad	bronchial
17	chr2:20100200-20102200	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr2:20100200-20102400	Active TSS	Esophagus	oesophagus
19	chr2:20100200-20102400	Active TSS	Left Ventricle	heart
20	chr2:20100200-20102400	Active TSS	Stomach Mucosa	stomach
21	chr2:20100200-20102600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:20100200-20102600	Active TSS	Fetal Muscle Trunk	muscle
23	chr2:20100200-20102800	Active TSS	Colonic Mucosa	Colon
24	chr2:20100400-20102200	Active TSS	Rectal Smooth Muscle	rectum
25	chr2:20100400-20102400	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr2:20100400-20102400	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr2:20100400-20102400	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr2:20100400-20102400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr2:20100400-20102400	Active TSS	Small Intestine	intestine
30	chr2:20100400-20102400	Bivalent/Poised TSS	HepG2	liver
31	chr2:20100400-20102400	Active TSS	HMEC	breast
32	chr2:20100400-20102600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr2:20100400-20102600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:20100400-20102600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:20100400-20102600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:20100400-20102600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:20100400-20102600	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr2:20100400-20102600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr2:20100400-20102600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:20100400-20102600	Active TSS	Psoas Muscle	Psoas
41	chr2:20100400-20102800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr2:20100400-20102800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:20100400-20102800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:20100600-20102000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:20100600-20102200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:20100600-20102200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:20100600-20102200	Active TSS	Primary T cells fromperipheralblood	blood
48	chr2:20100600-20102200	Active TSS	Brain Angular Gyrus	brain
49	chr2:20100600-20102200	Active TSS	Gastric	stomach
50	chr2:20100600-20102200	Active TSS	Lung	lung

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